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Nucleic Acids Research 2004 32(13):4026-4032; doi:10.1093/nar/gkh729
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Published online 2 August 2004

Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved

Quantitative modeling of DNA–protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor

Tsz-Kwong Man, Joshua SungWoo Yang and Gary D. Stormo*

Department of Genetics, Washington University, 660 S. Euclid, Box 8232, St Louis, MO 63110, USA

* To whom correspondence should be addressed. Tel: +1 314 747 5534; Fax: +1 314 362 7855; Email: stormo{at}genetics.wustl.edu
Present address: Tsz-Kwong Man, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA

Received May 27, 2004; Revised and Accepted July 10, 2004

Understanding DNA–protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple fluorescence, relative affinity (QuMFRA) assay, we determine the binding specificity of 11 different position 6 variants of the Mnt repressor for operators containing all 16 possible dinucleotides at operator positions 16 and 17. We show that the wild-type and all variant proteins interact with the two positions in a non-independent manner, but that a simple independent model provides a close approximation to the true binding affinities. The wild-type His at amino acid 6 is the only protein to prefer the AC sequence of the wild-type operator, whereas most of the variant proteins prefer TA. H6R is unique in having a strong preference for C at position 16. A comparison of the quantitative binding data for all of the protein variants with a model for recognition of the early growth response (EGR) zinc finger family suggests that interactions of Mnt with positions 16 and 17 are similar to interactions of EGR with positions 1 and 2, respectively. This information leads to an augmented model for the interaction of Mnt with its operator.


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